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Normal livers, Matched non-tumor follow-up and HCV liver biopsy transcriptomes

We compared CHC biopsies (Baseline) with normal livers to identify HCV induced transcriptional changes. At the time of HCC diagnosis in the CHC-HCC group, we collected matched non-tumor liver biopsies. Additionally we acquired liver biopsies from patients not included in the study with an active HCV infection for risk score prediction. Snap frozen biopsies were crushed in liquid nitrogen. Total RNA was extracted using the ZR-Duet DNA and RNA MiniPrep Plus kit (Zymo Research) according to the manufacturer’s instructions. RNA sequencing was done in single-end mode on an Illumina HiSeq 2500 with 101 or 51 cycles. RNA-Seq and WES were performed at the Department of Biosystems Science and Engineering ETH Zurich, D-BSSE in Basel.

Type: RNASeq
Archive: European Genome-phenome Archive (EGA)

1 Dataset

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Dataset ID	Description	Technology	Samples
EGAD50000001591	We conducted a nested case–control study within a prospective liver biopsy biobank at the University Hospital Basel. Patients with chronic hepatitis C (CHC) who developed hepatocellular carcinoma (HCC) during follow-up (index cases, CHC-HCC) were identified and 1:2 propensity score-matched to CHC controls without HCC (controls, CHC-nonHCC). Matching included clinical, demographic, and virological risk factors for HCC. Liver biopsies were analyzed using RNA and whole-exome sequencing.	Illumina HiSeq 2500 Illumina NovaSeq 6000	139